args <- commandArgs(trailingOnly = TRUE) # read in command line parameter
setwd(args[1]) # set working directory to target folder

# leave the rest as is

enriched<-read.table("exome_enriched.txt")
depleted<-read.table("exome_depleted.txt")
enriched_count<-read.table("exome_count_enriched.txt")
depleted_count<-read.table("exome_count_depleted.txt")
enrichment<-round(sum(enriched_count$V1)/(sum(enriched_count$V1)+sum(depleted_count$V1)) * 100, digits = 2)

total<-sum(enriched$V1 >= -1.0)
one<-sum(enriched$V1 >= 1.0)
five<-sum(enriched$V1 >= 5.0)
ten<-sum(enriched$V1 >= 10.0)
twenty<-sum(enriched$V1 >= 20.0)
hundred<-sum(enriched$V1 >= 100.0)

pdf(file="SureSelect_Enrichment_Statistics.pdf", width=10, height=12)
layoutmat<-matrix(data=c(1,2), nrow=2, ncol=1, byrow=TRUE)
layout(layoutmat)

hist(round(depleted$V1), xlim=c(0,150), ylim=c(0,2000), breaks=1*0:4000, col = "red", xlab = "Mean coverage", main = paste(
        "SureSelect depleteded regions\n mean coverage: ",
        round(mean(depleted$V1), digits = 2) )
)

hist(round(enriched$V1), xlim=c(0,1000), ylim=c(0,40), breaks=1*0:1500, col = "blue", xlab = "Mean coverage", main = paste(
        "SureSelect enriched regions",
        "\n mean coverage: ", round(mean(enriched$V1), digits = 2),
        ", Specificity: ",  enrichment, "%",
        "\n Targets: ",  total,
        ", Cov >= 1: ", one,
        ", Cov >= 5: ", five,
        ", Cov >= 10: ", ten,
        ", Cov >= 20: ", twenty,
	"\n Cov >= 100: ", hundred)
)
dev.off()
